From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Feb 18 2014 - 16:04:23 CST
Sorry, I meant "not to calculate charges for your protein atoms".
On 18 February 2014 23:54, MEHRAN MB <mb.mehran1_at_gmail.com> wrote:
> You are right, but different states of residue could be made by apply
> patches using psfgen plug in too. These patches could change HIS to HID
> or GLU to GLUP and etc.
>
> -mehran
>
>
> On Tue, Feb 18, 2014 at 3:56 PM, Thomas Evangelidis <tevang3_at_gmail.com>wrote:
>
>> Protein force fields are developed to reproduce experimental observables.
>> The partial charges of amino acids are part of the force field, therefore
>> you must not change them. In that respect, you should use PDB2PQR just to
>> make assumptions about the protonation state of residues like HIS, ASP,
>> GLU, not to calculate changes for your protein atoms.
>>
>>
>> On 18 February 2014 22:30, zeynab mohamad hoseyni <zmhoseyni_at_yahoo.com>wrote:
>>
>>> Hi Mehran,
>>>
>>> I used the mentioned server to predict the protonation states of
>>> Histidine mainly. The server does it according to the Pka values
>>> calculated using the ProPka server.
>>> Histidine is one of the polar amino acids who are called titratable
>>> amino acids (
>>> http://enzyme.ucd.ie/main/index.php/Introduction_to_pKa_calculations).
>>> Note that in the CHARMM topology file the charges assigned to the atoms
>>> of each residues are fixed and for example all ARG residues are composed of
>>> atoms
>>> with fixed charges and doesn't matter where they are located while in
>>> reality the Pka values for the ARG residues placing on the surface of
>>> protein (facing waters)
>>> are different from those located in the interior of the protein (
>>> http://en.wikipedia.org/wiki/Protein_pKa_calculations). This means that
>>> the charge distribution has to
>>> be different for those ARG residues experiencing different
>>> environment. PQR contain the charge distribution for the atoms of
>>> residues according to the Pka calculation. So I was trying to use those
>>> partiol charges in my psf file..
>>> The HIS case is much more delicate as its Pka is closed to the PH of
>>> water. So any small changes in the PH could change the protonation
>>> state of HIS to be one of HSE,
>>> HSD or HSP. These are all I know...
>>>
>>> All the Best,
>>> Zeynab
>>>
>>>
>>> On Tuesday, February 18, 2014 4:10 PM, MEHRAN MB <mb.mehran1_at_gmail.com>
>>> wrote:
>>>
>>> Hi Zeynab,
>>>
>>> On Sun, Feb 16, 2014 at 10:54 AM, zeynab mohamad hoseyni <
>>> zmhoseyni_at_yahoo.com> wrote:
>>>
>>> Dear all,
>>> I use pdb2pqr (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) server to add
>>> hydrogen atoms to the protein structure.
>>>
>>>
>>> I have no experience in pdb2pqr, but it seems it is not designed to
>>> add hydrogen atoms
>>> "This server enables a user to convert PDB <http://www.rcsb.org/pdb/> files
>>> into PQR files. PQR files are PDB files where the occupancy and B-factor
>>> columns have been replaced by per-atom charge and radius."
>>>
>>>
>>> The server produces pqr file containing protein coordinates (including
>>> the hydrogen atoms) as well as the charges assigned to each atom.
>>> These charges are different from those provided by topology file
>>>
>>> if you could make psf file (probably using *AutoPSF plugin*) it should
>>> gave you pdb file including hydrogen atoms too. So I am not sure why you
>>> are using PQR?1?!
>>>
>>> -mehran
>>>
>>>
>>>
>>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> Thomas Evangelidis
>>
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>>
>> email: tevang_at_pharm.uoa.gr
>>
>> tevang3_at_gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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